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[phenixbb] PHENIX 1.24.1 beta now available

by Paul Adams

======================================================================= PHENIX 1.24.1 Beta Release ======================================================================= On behalf of the PHENIX development team I am happy to announce that the next general release version of PHENIX is now available. Binary installers for Linux, SGI and Tru64 platforms are available at our download site: http://phenix-online.org/download/ Current users of PHENIX should upgrade to this most recent release version. To obtain download instructions visit: http://phenix-online.org/phenix_request/ Documentation for PHENIX is available at: http://phenix-online.org/download/documentation/phenix/ There is a PHENIX mailing list at: http://www.phenix-online.org/mailman/listinfo/phenixbb/ There is a PHENIX wiki at: http://www.phenix-online.org/phenix_wiki Please consult the installer README file or online documentation for installation instructions. This is a beta test version, and we therefore look forward to feedback and bug reports from users. Please direct questions and problem reports to: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to PHENIX should visit the PHENIX website for information about the PHENIX Industrial Consortium: http://www.phenix-online.org/ This version of PHENIX has three main user interfaces: command-line tools, strategies and wizards. Wizards are available under the Wizard tab in the PHENIX GUI, and are designed to complete a complex structure determination process, making automatic decisions when possible, but prompting the user for additional information when necessary. Strategies are available under the Strategy tab in the PHENIX GUI, and are networks of tasks constructed to perform higher-level functions. Version 1.24.1b of PHENIX includes: Wizards (in the PHENIX GUI and from the command-line) ===================================================== - AutoSol - automated structure solution (from processed data to a first map and model) using HySS, SOLVE, RESOLVE, and phenix.refine. - AutoMR - automated molecular replacement, using PHASER. Followed by automated model rebuilding using the AutoBuild wizard. - AutoBuild - automated model building or rebuilding combined with structure refinement, using RESOLVE and phenix.refine. - AutoLig - automated ligand fitting into difference density maps using RESOLVE once a complete protein model is available. Strategies (in the PHENIX GUI) ============================== - Ligand screening against the top 200 ligands in the PDB, using RESOLVE. - Structure solution (MAD/SAD and SIR(AS)/MIR(AS)) combining HySS, SOLVE and RESOLVE. - Phase improvement using maximum likelihood methods in RESOLVE. - Model building using TEXTAL or RESOLVE. Command-line tools ================== - mmtbx.xtriage (comprehensive data quality assessment, including twin analysis) - iotbx.reflection_statistics (analysis of diffraction data) - mmtbx.fest (FA value calculation) - phenix.hyss (anomalous substructure determination) - textal.build (automated model building with TEXTAL) - elbow.builder (generation of ligand coordinates and restraints) - phenix.refine (automated structure refinement) - phenix.geometry_minimization (regularize a structure) - phenix.solve (solve) - phenix.resolve (resolve) - phenix.resolve_pattern (resolve_pattern) - iotbx.mtz.dump (write useful information about a MTZ file) - iotbx.pdb.hierarchy (write useful information about a PDB file) Citing PHENIX ============= If you use PHENIX for solving a structure please cite this publication: PHENIX: building new software for automated crystallographic structure determination P.D. Adams, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter and T.C. Terwilliger. Acta Cryst. D58, 1948-1954 (2002). PHENIX Developers ================= Lawrence Berkeley National Laboratory - Paul D. Adams - Pavel Afonine - Ralf W. Grosse-Kunstleve - Nigel W. Moriarty - Nicholas K. Sauter - Peter H. Zwart Los Alamos National Laboratory - Tom C. Terwilliger - Li-Wei Hung - Thiru Radhakannan University of Cambridge - Randy J. Read - Airlie J. McCoy - Laurent C. Storoni Texas A&M University - Jim C. Sacchettini - Tom R. Ioerger - Kresha Gopal - Lalji Kanbi - Erik McKee - Reetal K. Pai - Tod D. Romo - Jacob N. Smith Acknowledgements ================ We are very grateful to the following for making code or libraries available to us: - Alexei Vagin and Garib Murshudov for the CCP4 Monomer Library. - The CCP4 developers for making the MTZ library available to us. - Kevin Cowtan for contributing to the cctbx reciprocal space asymmetric units. - David Abrahams for developing the Boost.Python library. Funding ======= The development of PHENIX is principally funded through the Protein Structure Initiative of the National Institute of General Medical Sciences (NIH) under grant P01GM063210. For further information about the Protein Structure Initiative please visit: http://www.nigms.nih.gov/psi/ We also acknowledge the generous support of the members of the PHENIX Industrial Consortium. For more details please visit: http://www.phenix-online.org/ ======================================================================= PHENIX 1.24.1 Beta Release ======================================================================= -- ========================================================== | Paul Adams, | | Senior Staff Scientist, Physical Biosciences Division | | Head, Berkeley Center for Structural Biology | | Deputy PI, Berkeley Structural Genomics Center | |--------------------------------------------------------| | Building 64, Room 248 | Lawrence Berkeley Laboratory, | | Tel: 510-486-4225 | 1 Cyclotron Road, | | FAX: 510-486-5909 | BLDG 64R0121, | | mailto:[email protected] | Berkeley, CA 94720, USA. | ==========================================================

18 years, 11 months

Re: [phenixbb] TRIED resolve ...NEED A BIGGER VERSION... message

by Tom Terwilliger

Hi Felix, Well almost. It will activate the right size if it exists in the distribution that you have. The normal extra_huge version is "isizeit = 36" which is 6 x the standard size. If that is not big enough autobuild will stop. I can provide bigger versions if you need them (and then they will automatically be used). All the best, Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss On Jan 5, 2009, at 8:36 AM, Felix Frolow wrote: > Tom, does it mean that for structure of ANY size the right version > of RESOLVE will be activated now automatically? > If it does, it is very important improvement > FF > Dr Felix Frolow > Professor of Structural Biology and Biotechnology > Department of Molecular Microbiology > and Biotechnology > Tel Aviv University 69978, Israel > > Acta Crystallographica D, co-editor > > e-mail: mbfrolow(a)post.tau.ac.il > Tel: ++972 3640 8723 > Fax: ++972 3640 9407 > Cellular: ++972 547 459 608 > > On Jan 5, 2009, at 5:25 PM, Tom Terwilliger wrote: > >> Hi Ben, >> Yes, that is just FYI. There are a few sizes of resolve and this >> means the smallest wasn't big enough. I'll change the message so >> that it is more informative... >> All the best, >> Tom T >> >> >> >> Thomas C. Terwilliger >> Mail Stop M888 >> Los Alamos National Laboratory >> Los Alamos, NM 87545 >> >> Tel: 505-667-0072 email: terwilliger(a)LANL.gov >> Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov >> PHENIX web site: http:www.phenix-online.org >> ISFI Integrated Center for Structure and Function Innovation web >> site: http://techcenter.mbi.ucla.edu >> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB >> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss >> >> >> >> >> On Jan 5, 2009, at 8:09 AM, Ben Eisenbraun wrote: >> >>> >>> Howdy Phenixians, >>> >>> One of my users is running phenix.autobuild, and while it seems to >>> run >>> okay, the output contains this warning: >>> >>> TRIED resolve ...NEED A BIGGER VERSION... >>> >>> Looking through phenix/phenix/autosol/run_resolve.py, it seems >>> like this >>> is an informational message, but I'm not sure, so I figured I'd ask. >>> >>> Is this actually an error? >>> >>> This is phenix-1.3-final on OS X 10.5. >>> >>> Thanks. >>> >>> -ben >>> >>> -- >>> Ben Eisenbraun >>> Structural Biology Grid Harvard Medical >>> School >>> http://sbgrid.org http://hms.harvard.edu >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb

16 years, 5 months

Re: [phenixbb] calculate Fc for the whole unit cell from a Fc of a single symmetric unit.

by zhangh1＠umbc.edu

Thanks a lot! > We can expand reciprocal-space arrays, too, with the > cctbx.miller.array.expand_to_p1() > method. You can use it from the command line via > > phenix.reflection_file_converter --expand-to-p1 ... > > See also: > http://www.phenix-online.org/documentation/reflection_file_tools.htm > > Ralf > > > On Mon, Jul 11, 2011 at 10:56 AM, <zhangh1(a)umbc.edu> wrote: > >> Sorry I haven't got a chance to check my email recently. >> >> Yes, I meant expansion to P1. The thing is cctbx relies on the atomic >> model I think, but I only have model Fc available. >> >> Hailiang >> >> > I suspect what Hailang means is expansion into P1. >> > >> > I am sure this can be accomplished through some either existing or >> > easily coded cctbx tool. However, when I looked into a different task >> > recently that included P1 expansion as a step, I learned that SFTOOLs >> > can do this, albeit there was a bug there which caused trouble in >> > certain space groups (may be fixed by now so check if there is an >> > update). >> > >> > Hailang - if P1 expansion is what you need, I could share my own code >> as >> > well, let me know if that is something you want to try. >> > >> > Cheers, >> > >> > Ed. >> > >> > On Fri, 2011-07-08 at 14:44 -0700, Ralf Grosse-Kunstleve wrote: >> >> Did you get responses already? >> >> If not, could you explain your situation some more? >> >> We have algorithms that do the symmetry summation in reciprocal >> space. >> >> The input is a list of Fc in P1, based on the unit cell of the >> >> crystal. Is that what you have? >> >> Ralf >> >> >> >> On Wed, Jul 6, 2011 at 1:38 PM, <zhangh1(a)umbc.edu> wrote: >> >> Hi, >> >> >> >> I am wondering if I only have structure factors calculated >> >> from a single >> >> symmetric unit, is there any phenix utility which can >> >> calculate the >> >> structure factor for the whole unit cell given the symmetric >> >> operation or >> >> space group and crystal parameters? Note I don't have an >> >> atomic model and >> >> only have Fc. >> >> >> >> Thanks! >> >> >> >> Hailiang >> >> >> >> _______________________________________________ >> >> phenixbb mailing list >> >> phenixbb(a)phenix-online.org >> >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> >> >> >> >> _______________________________________________ >> >> phenixbb mailing list >> >> phenixbb(a)phenix-online.org >> >> http://phenix-online.org/mailman/listinfo/phenixbb >> > >> > >> > _______________________________________________ >> > phenixbb mailing list >> > phenixbb(a)phenix-online.org >> > http://phenix-online.org/mailman/listinfo/phenixbb >> > >> > >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

13 years, 11 months

[phenixbb] Re: for autobuild full sequence?

by Pavel Afonine

Hi James, Yes, that makes sense, and it’s what I suspected. Creating a string of residues that matches your sequence is, as I mentioned, a ten-minute exercise in CCTBX. However, ensuring that it folds within the allowed volume, avoids self-clashes, and meets other geometric quality metrics is a more complex challenge—but not impossible. My approach would be to create a map where all voxels occupied by existing atoms have negative values. Then, assuming the start and end points of your chain are known, I’d generate a rough path through non-negative voxels. From there, a round of real-space simulated annealing could refine the structure. But that’s starting to sound like a full project now! Pavel On 4/1/25 13:23, James Holton wrote: > Yes, but I don't want it to clash with other molecules in the unit > cell, including itself. > > When I was an undergrad, Steve Mayo called this an "amorphous > builder". Trivial in concept, but you need to do a "bump check" after > adding each atom, and then have a plan for what to do if you hit a bump. > > Make sense? > > -James > > > On 4/1/2025 1:10 PM, Pavel Afonine wrote: >> Hi James, >> >> Are you just looking to string residues together in a line from start >> to end according to your sequence? That’s a quick 10-minute exercise >> using CCTBX, but I suspect that’s not exactly what you need. >> >> Pavel >> >> On 4/1/25 12:28, Tom Terwilliger wrote: >>> Hi James, >>> I think there is no way to force AutoBuild to build a full sequence >>> when there is no density. >>> All the best, >>> Tom T >>> >>> >>> On Tue, Apr 1, 2025 at 10:26 AM James Holton <jmholton(a)lbl.gov> wrote: >>> >>> Hey all, >>> >>> Don't worry, nothing is funny today. I have a real question: >>> >>> Is there a way to force phenix.autobuild to build in the entire >>> sequence? As in: the full length of the actual molecule that is >>> in the >>> crystal, such as what is supposed to go into SEQRES, regardless of >>> "visible" density? I am trying to come up with a pipeline for >>> prepping >>> MD simulations of protein crystals. It seems proper to me that the >>> molecule being simulated should be the actual molecular species, >>> disordered bits an all. However, we don't seem to have good >>> technology >>> for building protein chains into "nothingness". Yes, I know >>> Alphafold is >>> a thing, but it is rubbish at clashes in the context of a crystal. >>> >>> I mean, I could write something, but does this tool already exist? >>> >>> Cheers, and happy Tuesday, >>> >>> -James Holton >>> MAD Scientist >>> >>> >>> _______________________________________________ >>> phenixbb mailing list -- phenixbb(a)phenix-online.org >>> To unsubscribe send an email to phenixbb-leave(a)phenix-online.org >>> Unsubscribe: phenixbb-leave@%(host_name)s >>> >>> >>> >>> -- >>> Thomas C Terwilliger >>> Laboratory Fellow, Los Alamos National Laboratory >>> Senior Scientist, New Mexico Consortium >>> 100 Entrada Dr, Los Alamos, NM 87544 >>> Email: tterwilliger(a)newmexicoconsortium.org >>> Tel: 505-431-0010 >>> >>> >>> _______________________________________________ >>> phenixbb mailing list --phenixbb(a)phenix-online.org >>> To unsubscribe send an email tophenixbb-leave(a)phenix-online.org >>> Unsubscribe: phenixbb-leave@%(host_name)s >

3 months

[phenixbb] Re: Simulate map from model

by Ricardo Righetto

Dear all, Thanks a lot for your replies! After playing a bit with the suggested command line programs I decided to follow Robert's suggestion and go the Python way, hoping to gain finer control of the options. I am using the attached Python script to calculate an exact map from a model, using electron scattering table. When running, for example, on 4v7t.cif I get a map that looks as follows (orthogonal central slices): [image: image.png] And the MRC header as read by IMOD is: RO image file on unit 1 : fourier_map.mrc Size= 32401 K Number of columns, rows, sections ..... 320 240 108 Map mode .............................. 2 (32-bit float) Start cols, rows, sects, grid x,y,z ... 0 0 0 108 240 320 Pixel spacing (Angstroms).............. 1.958 1.809 1.941 Cell angles ........................... 90.000 90.000 90.000 Fast, medium, slow axes ............... Z Y X Origin on x,y,z ....................... 0.000 0.000 0.000 Minimum density ....................... 0.0000 Maximum density ....................... 2.5699 Mean density .......................... 0.12004E-01 RMS deviation from mean................ 0.47980E-01 tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0 Space group,# extra bytes,idtype,lens . 19 0 0 0 1 Titles : Some text With these in mind, I have some questions: 1) If I understand correctly, the map contains exactly one unit cell as defined in the .cif file. How can I choose a different assembly to generate the map from? Say, biological (author-defined) assembly #1? 2) The pixel size is approximately the step I give to maptbx.crystal_gridding() but is not exactly isotropic. How can I enforce it as such? 3) Probably related to the question above, the box size is not cubic, I guess because of the unit cell dimensions. Since most cryo-EM programs expect maps to be cubic and have isotropic pixel sizes, I would like to enforce the final map to be sampled on a cubic grid. How can I do that? 4) Not exactly a question but what might be a bug report. When I use a model that was originally calculated based on a cryo-EM map (PDB entries I tried: 7k00, 7b75) I get the following error because the files have no crystal symmetry defined: Traceback (most recent call last): File "phenix_simulate_map.py", line 18, in <module> model.setup_scattering_dictionaries(scattering_table="electron") File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Phenix/phenix-1.21-5207/modules/cctbx_project/mmtbx/model/model.py", line 2398, in setup_scattering_dictionaries self.neutralize_scatterers() File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Phenix/phenix-1.21-5207/modules/cctbx_project/mmtbx/model/model.py", line 2821, in neutralize_scatterers xrs = self.get_xray_structure() File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Phenix/phenix-1.21-5207/modules/cctbx_project/mmtbx/model/model.py", line 478, in get_xray_structure assert cs is not None AssertionError Thanks in advance for your help again. I hope I'm not kicking too much of a can of worms here. Best wishes, -- Ricardo Diogo Righetto Em qua., 2 de abr. de 2025 às 21:12, Alexandre OURJOUMTSEV <sacha(a)igbmc.fr> escreveu: > Hi everybody, > > > > Inversely to what Pavel wrote, just if you want to get a > limited-resolution map of the Coulomb potential (and not anything else), > eventually with a resolution that varies over the map regions, Section 5.2 > of the manuscript > > > > https://arxiv.org/abs/2412.14350 > > > > exactly explains how to do this. I guess, if this critical, Phenix teams > can routinely add such an option. > > > > With best wishes, > > > > Sacha Urzhumtsev > > > > *De :* Pavel Afonine <pafonine(a)lbl.gov> > *Envoyé :* mercredi 2 avril 2025 20:54 > *À :* James Holton <jmholton(a)lbl.gov>; phenixbb(a)phenix-online.org; > ricardorighetto(a)gmail.com > *Objet :* [phenixbb] Re: Simulate map from model > > > > Hi, > > additionally: > > - If you want an exact map (not a finite-resolution Fourier map), use: > > phenix.model_map model.pdb scattering_table=electron > > - We are close to making a multipolar model available for density > calculations, which—if I understand correctly—is what you need to simulate > Coulomb potential maps. This feature is not yet available to general Phenix > users, but if you send me the model off-list, I can generate and send the > map back to you. > > Pavel > > On 4/2/25 10:52, James Holton wrote: > > Ostensibly, all you need to do is run phenix.fmodel with > scattering_table=electron . And perhaps try to come up with what k_sol > should be for the bulk solvent density. There are caveats, of course, not > the least of which is that, last I checked, the modified scattering from > formal charges like ions vs neutral groups is not implemented. I don't > actually know of a program that handles things like charges. I've heard > rumors that someone was working on full QM calculations of electrons moving > through matter to try and get this "right", but I have not heard about any > progress for some time. > > Sorry can't be more helpful, > > -James > > On 4/2/2025 4:52 AM, Ricardo Righetto wrote: > > Hi, > > > > Apologies if I'm missing something obvious, but I was not able to find > this in the documentation: is there a PHENIX tool for simulating Coulomb > potential maps (aka "cryo-EM maps") from atomic models? > > > > I'm looking for something like the molmap > <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html> > command in ChimeraX, but more accurate. One such alternative is the > simulate program from cisTEM, but I figured PHENIX might also have > something? > > > > Thank you! > > > > -- > Ricardo Diogo Righetto > > > > _______________________________________________ > > phenixbb mailing list -- phenixbb(a)phenix-online.org > > To unsubscribe send an email to phenixbb-leave(a)phenix-online.org > > Unsubscribe: phenixbb-leave@%(host_name)s > > > > > _______________________________________________ > > phenixbb mailing list -- phenixbb(a)phenix-online.org > > To unsubscribe send an email to phenixbb-leave(a)phenix-online.org > > Unsubscribe: phenixbb-leave@%(host_name)s > >

3 months

Re: [phenixbb] Using LigandFit to identify unknown density

by Maia Cherney

Hi Pavel, Peter, Thank you for your reply. My question is if the phenix.refine actually uses the B-factor restraints in the occupancy refinement. I did not give any restraints, so it should happen automatically? I like the idea that Peter mentioned that the restraints should make B -factors similar to surrounding molecules. Again, my question is does phenix.refine actually uses this approach? Maia Pavel Afonine wrote: > Hi Maia, > > first, I agree with Peter - the B-factor restraints should help, indeed. > > Second, I think we discussed this subject already on November 25, 2009: > > Subject: Re: [phenixbb] occupancy refinement > Date: 11/25/09 7:38 AM > > and I believe I didn't change my mind about it since that. I'm > appending that email conversation to the bottom of this email. > > Overall, if you get good 2mFo-DFc map and clear residual mFo-DFc map, > and ligand's B-factors are similar or slightly larger than those of > surrounding atoms, and refined occupancy looks reasonable, then I > think you are fine. > > Pavel. > > > On 1/27/10 2:05 PM, Maia Cherney wrote: >> Hi Pavel, >> >> I have six ligands at partial occupacies in my structure. >> Simultaneous refinement of occupancy and B factors in phenix gives a >> value of 0.7 for the ligand occupancy that looks reasonable. >> How does phenix can perform such a refinement given the occupancies >> and B factors are highly correlated? Indeed, you can >> increase/decrease the ligand occupancies while simultaneously >> increacing/decreasing their B factors without changing the R factor >> value. What criteria does phenix use in such a refinement if R factor >> does not tell much? >> >> Maia > > ******* COPY (11/25/09)************ > > > > On 11/25/09 7:38 AM, Maia Cherney wrote: >> Hi Pavel, >> >> It looks like all different refined occupancies starting from >> different initial occupancies converged to the same number upon going >> through very many cycles of refinement. >> >> Maia >> >> >> Pavel Afonine wrote: >> >>> Hi Maia, >>> >>> the atom parameters, such as occupancy, B-factor and even position >>> are interdependent in some sense. That is, if you have somewhat >>> incorrect occupancy, that B-factor refinement may compensate for it; >>> if you misplaced an atom the refinement of its occupancy or/and >>> B-factor will compensate for this. Note in all the above cases the >>> 2mFo-DFc and mFo-DFc maps will appear almost identical, as well as >>> R-factors. >>> >>> So, I think your goal of finding a "true" occupancy is hardly >>> achievable. >>> >>> Although, I think you can approach it by doing very many refinements >>> (say, several hundreds) (where you refine occupancies, B-factors and >>> coordinates) each refinement starting with different occupancy and >>> B-factor values, and make sure that each refinement converges. Then >>> select a subset of refined structures with similar and low R-factors >>> (discard those cases where refinement got stuck for whatever reason >>> and R-factors are higher) (and probably similar looking 2mFo-DFc and >>> mFo-DFc maps in the region of interest). Then see where the refined >>> occupancies and B-factors are clustering, and the averaged values >>> will probably give you an approximate values for occupancy and B. I >>> did not try this myself but always wanted to. >>> >>> If you have a structure consisting of 9 carbons and one gold atom, >>> then I would expect that the "second digit" in gold's occupancy >>> would matter. However, if we speak about dozen of ligand atoms >>> (which are probably a combination of C,N,O) out of a few thousands >>> of atoms of the whole structure, then I would not expect the "second >>> digit" to be visibly important. >>> >>> Pavel. >>> >>> >>> On 11/24/09 8:08 PM, chern wrote: >>> >>>> Thank you Kendall and Pavel for your responces. >>>> I really want to determine the occupancy of my ligand. I saw one >>>> suggestion to try different refinements with different occupancies >>>> and compare the B-factors. >>>> The occupancy with a B-factor that is at the level with the average >>>> protein B-factors, is a "true" occupancy. >>>> I also noticed the dependence of the ligand occupancy on the >>>> initial occupancy. I saw the difference of 10 to 15%, that is why I >>>> am wondering if the second digit after the decimal point makes any >>>> sence. >>>> Maia >>>> >>>> ----- Original Message ----- >>>> *From:* Kendall Nettles <mailto:[email protected]> >>>> *To:* PHENIX user mailing list <mailto:[email protected]> >>>> *Sent:* Tuesday, November 24, 2009 8:22 PM >>>> *Subject:* Re: [phenixbb] occupancy refinement >>>> >>>> Hi Maia, >>>> I think the criteria for occupancy refinement of ligands is >>>> similar to a decision to add an alt conformation for an amino >>>> acid. I don’t refine occupancy of a ligand unless the difference >>>> map indicates that we have to. Sometimes part of the igand may be >>>> conformationally mobile and show poor density, but I personally >>>> don’t think this justifies occupancy refinement without evidence >>>> from the difference map. I agree with Pavel that you shouldn’t >>>> expect much change in overall statistics, unless the ligand has >>>> very low occupancy., or you have a very small protein. We >>>> typically see 0.5-1% difference in R factors from refining with >>>> ligand versus without for nuclear receptor igand binding domains >>>> of about 250 amino acids, and we see very small differences from >>>> occupancy refinement of the ligands. >>>> >>>> Regarding the error, I have noticed differences of 10% percent >>>> occupancy depending on what you set the starting occupancy before >>>> refinement. That is, if the starting occupancy starts at 1, you >>>> might end up with 50%, but if you start it at 0.01, you might get >>>> 40%. I don’t have the expertise to explain why this is, but I >>>> also don’t think it is necessarily important. I think it is more >>>> important to convince yourself that the ligand binds how you >>>> think it does. With steroid receptors, the ligand is usually >>>> planer, and tethered by hydrogen bonds on two ends. That leaves >>>> us with with four possible poses, so if in doubt, we will dock in >>>> the ligand in all of the four orientations and refine. So far, we >>>> have had only one of several dozen structures where the ligand >>>> orientation was not obvious after this procedure. I worry about a >>>> letter to the editor suggesting that the electron density for the >>>> ligand doesn’t support the conclusions of the paper, not whether >>>> the occupancy is 40% versus 50%. >>>> >>>> You might also want to consider looking at several maps, such as >>>> the simple or simulated annealing composite omit maps. These can >>>> be noisy, so also try the kicked maps ( >>>> >>>> http://www.phenix-online.org/pipermail/phenixbb/2009-September/002573.html), >>>> >>>> >>>> <http://www.phenix-online.org/pipermail/phenixbb/2009-September/002573.html%…,> >>>> >>>> which I have become a big fan of. >>>> >>>> Regards, >>>> Kendall Nettles >>>> >>>> On 11/24/09 3:07 PM, "chern(a)ualberta.ca" <chern(a)ualberta.ca> >>>> wrote: >>>> >>>> Hi, >>>> I am wondering what is the criteria for occupancy >>>> refinement of >>>> ligands. I noticed that R factors change very little, but the >>>> ligand >>>> B-factors change significantly . On the other hand, the >>>> occupancy is >>>> refined to the second digit after the decimal point. How can >>>> I find >>>> out the error for the refined occupancy of ligands? >>>> >>>> Maia >>>> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > >

15 years, 5 months

Re: [phenixbb] Error determining reference matches

by Pavel Afonine

Hi Dan, the only way we can help (= debug the problem, fix it or/and suggest a work-around) is if we can reproduce it here locally. To do this we need all inputs and commands necessary to reproduce the refinement run that crashed. Please send files to me (not to whole mailing list) and I will look myself or redirect to a respective developer. Thanks, Pavel On 8/30/13 4:32 PM, Dan McNamara wrote: > Hi all, > > I am encountering a strange crash when running phenix.refine through > the command line with reference model restraints turned on. The > references point to two different PDB files, one labeled as chain A > and one labeled as chain B. > > This error occurs whether I have my refinement model in P1 with 192 > chains or P2(1) with 96 chains. The chains are A-EZ (192) or A-BH > (96). It appears to fail to align the reference models to the > sequences in the refinement model. This error does not occur with > other smaller target structures under 25 chains and reference models > used with the same installation of phenix. > > I am hoping for any advice on why this might be happening or how I > might get around it. > > ================== Extract refinement strategy and selections > ================= > > Refinement flags and selection counts: > individual_sites = True (401472 atoms) > torsion_angles = False (0 atoms) > rigid_body = True (401472 atoms in 192 groups) > individual_adp = False (iso = 0 aniso = 0) > group_adp = True (201984 atoms in 25824 groups) > tls = False (0 atoms in 0 groups) > occupancies = False (0 atoms) > group_anomalous = False > > n_use = 401472 > n_use_u_iso = 401472 > n_use_u_aniso = 0 > n_grad_site = 0 > n_grad_u_iso = 0 > n_grad_u_aniso = 0 > n_grad_occupancy = 0 > n_grad_fp = 0 > n_grad_fdp = 0 > total number of scatterers = 401472 > *** Adding Reference Model Restraints *** > determining reference matches automatically... > Traceback (most recent call last): > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", > line 11, in <module> > command_line.run(command_name="phenix.refine", args=sys.argv[1:]) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/phenix/phenix/refinement/command_line.py", > line 92, in run > master_params=customized_master_params) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/phenix/phenix/refinement/driver.py", > line 501, in __init__ > log=self.log) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", > line 147, in __init__ > self.get_reference_dihedral_proxies() > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", > line 460, in get_reference_dihedral_proxies > log=self.log) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", > line 323, in process_reference_groups > moving_chain = mod_h) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/utils.py", > line 426, in _ssm_align > ssm_alignment = ccp4io_adaptbx.SSMAlignment.residue_groups(match=ssm) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", > line 215, in residue_groups > return cls( match = match, indexer = indexer ) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", > line 176, in __init__ > self.pairs.append( ( get( f, indexer1 ), get( s, indexer2 ) ) ) > File > "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", > line 173, in get > assert identifier in indexer, "Id %s missing" % str( identifier ) > AssertionError: Id ('A', 1, ' ') missing > > Best, > Dan > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

11 years, 10 months

Re: [phenixbb] measuring the angle between two DNA duplexes

by Pavel Afonine

Hi Tim, thanks for the reference! There is a number of instances where this approach is useful. In Phenix this is also used to determine density map peak sphericity (see cctbx/maptbx/sphericity.h) and to get initial values for refinement of anisotropic ADPs from map peaks. Sure I will play with this and visit as many corner cases as I could think of! All the best, Pavel On 1/21/14, 1:25 AM, Tim Gruene wrote: > Hi Pavel, > > that's the method described in > http://journals.iucr.org/a/issues/2011/01/00/sc5036/index.html ;-) based > on the moments of inertia (a computer scientist might name it > differently). I am not sure, though, you would get the desired result > for short helices. E.g. a helix defined by three atoms the eigenvalue > would point roughly in the direction of the external phosphates, which > is far from parallel with the helix axis. > > Best, > Tim > > On 01/21/2014 04:20 AM, Pavel Afonine wrote: >> Hi Ed, >> >> interesting idea! Although I was thinking to have a tool that is a >> little more general and a little less context dependent. Say you have >> two clouds of points that are (thinking in terms of macromolecules) two >> alpha helices (for instance), and you want to know the angle between the >> axes of the two helices. How would I approach this?.. >> >> First, for each helix I would compute a symmetric 3x3 matrix like this: >> >> sum(xn-xc)**2 sum(xn-xc)*(yn-xc) sum(xn-xc)*(zn-zc) >> sum(xn-xc)*(yn-xc) sum(yn-yc)**2 sum(yn-yc)*(yz-zc) >> sum(xn-xc)*(zn-zc) sum(yn-yc)*(yz-zc) sum(zn-zc)**2 >> >> where (xn,yn,zn) is the coordinate of nth atom, the sum is taken over >> all atoms, and (xc,yc,zc) is the coordinate of the center of mass. >> >> Second, for each of the two matrices I would find its eigen-values and >> eigen-vectors, and select eigen-vectors corresponding to largest >> eigenvalues. >> >> Finally, the desired angle is the angle between the two eigen-vectors >> found above, which is computed trivially. >> I think this a little simpler than finding the best fit for a 3D line. >> >> What you think? >> >> Pavel >> >> >> On 1/20/14, 2:14 PM, Edward A. Berry wrote: >>> >>> Pavel Afonine wrote: >>> . . >>> >>>> The underlying procedure would do the following: >>>> - extract two sets of coordinates of atoms corresponding to two >>>> provided atom selections; >>>> - draw two optimal lines (LS fit) passing through the above sets >>>> of coordinates; >>>> - compute and report angle between those two lines? >>>> >>> This could be innacurate for very short helices (admittedly not the >>> case one usually would be looking for angles), or determining the axis >>> of a short portion of a curved helix. A more accurate way to >>> determine the axis- have a long canonical duplex constructed with its >>> axis along Z (0,0,1). Superimpose as many residues of that as required >>> on the duplex being tested, using only backbone atoms or even only >>> phosphates. Operate on (0,0,1) with the resulting operator (i.e. take >>> the third column of the rotation matrix) and use that as a vector >>> parallel to the axis of the duplex being tested. >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

11 years, 5 months

Re: [phenixbb] alternatives to RMSD

by Tim Gruene

Hi Pavel, if the B-value would correspond to a cloud of possible locations, one should be able to move an atom within the cloud without altering the R-value and other quality indicators and without a refinement program moving the atom back to where it came from. In my experience this is not the case, why I prefer the (original) scientific interpretation of the B-value as to model of harmonic motion rather than its statistical. That is also the reason why I am not a friend of exorbital B-values in PDB-files. I think they tend to fudge poor modelling. Cheers, Tim On 07/07/2014 10:02 PM, Pavel Afonine wrote: > Hi Tim, > > consider two atoms located at say 1A distance apart. In one case their > B-factors are 1A**2 and in the second case their B-factors are 100A**2. > In the first case these are two individual atoms and measuring distance > between them makes sense, while in the second case atoms virtually > coincide (within the cloud of their possible locations, given their > B-factor) and therefore measuring distance between them isn't very > meaningful. Using the map would differentiate these two scenarios, while > usual way of computing RMSD would not. I guess this is what I was trying > to say in my previous post. > > Whether the values of a metric of choice are intuitive or not is a > separate question. After all you can always calibrate your expectations > using examples with known answer. > > Pavel > > > On 7/7/14, 3:47 AM, Tim Gruene wrote: >> Hi Patrick, >> >> why don't you superimpose only the matching segments and report their >> RMSD? It is the common procedure for RMSD's from superpositions to >> report the aligned residues together with the RMSD. >> >> The advantage compared to a map CC is similar to that of R_sym over >> R_meas: readers have a better concept (from experience) of what the >> numbers mean. >> >> Best, >> Tim >> >> On 07/02/2014 05:15 PM, Patrick. C wrote: >>> Hi Phenix users, >>> >>> I am not a crystallographer but I though you guys might be a good >>> place to ask >>> this question. >>> >>> I have 2 super secondary structures, A and B and they consist of >>> Helix-turn-Strand >>> >>> Due to the turn the two structures have a poor RMSD because the two >>> flanking >>> fragments of Helix and Strand are far from each other but when I >>> superimpose the >>> two fragments individually(helixA with helix B and standA with >>> strandB in Pymol >>> they align very well). >>> >>> Now, is there a way to express this instead of using the RMSD? >>> When the two structures align well the RMSD is very good but a slight >>> movement >>> and the RMSD is awful. >>> But looking at the two structures I can see they follow the same path >>> through space. >>> >>> Thank you, >>> Patrick >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> 3D Earth Screensaver Preview <http://www.inbox.com/earth> >>> *Free 3D Earth Screensaver* >>> Watch the Earth right on your desktop! Check it out at >>> www.inbox.com/earth >>> <http://www.inbox.com/earth> >>> >>> >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

10 years, 11 months

Re: [phenixbb] Coot mutation of Asp residue to isoAsp residue

by Xiao Lei

Hi Zhejie, For the 1AT6 structure, I downloaded its density in coot using "fetch density from EDS", but when I found the IAS at 101 position and try to do real space refine, it gives an error that "Refinement setup failure. Failed to find restraints for IAS." I do not know how to fix this but it seems to me it's caused by incomplete restraints dictionary or monomer library in ccp4? Thanks. Xiao On Tue, Aug 18, 2015 at 10:42 AM, Xiao Lei <xiaoleiusc(a)gmail.com> wrote: > Hi Zhijie, > > Thank you very much for the information. For step 1 you mentioned, I can > get monomer with L-Asp but it seems I can not drag it (or I do not know how > to do) and can not delete or modify it to become isoAsp. I will try play > around more though. > > Xiao > > On Mon, Aug 17, 2015 at 6:33 PM, Zhijie Li <zhijie.li(a)utoronto.ca> wrote: > >> Hi Xiao, >> >> IsoAsp is essentially an L-Asp linked with next aa through its side chain >> (beta) carboxyl. So the mutation button won’t help you. You need to build >> in a new L-ASP, which is treated as a covalently linked ligand (HETATM >> records), instead of a standard residue (ATOM records) of the protein chain. >> >> A practical method might be: 1) delete the original Asp, 2) import a free >> L-Asp using “get monomer”, delete its hydrogen atoms and drag it into the >> density, delete one oxygen atom on the beta-carboxyl and change the >> residue’s numbering and chain id to fit it into the sequence, 3) edit the >> PDB, if necessary, to turn the ASP into a ligand (a HETATM record inside >> the chain). >> >> For step 3, you may need to rename the ASP to something else (IAS was >> used for isoASP in older pdb, so I would go with IAS ) so that coot won’t >> try to make a regular peptide bond using its main chain carboxyl during >> real space refinement. Of course you will need to make a cif file for the >> “new” compound too. I guess you can make a copy of ASP.cif from the monomer >> library and change everything in it to IAS. I think if you have placed the >> IAS to the right location and its ends are in bonding distance with the >> neighbouring aa residues you may not need to do anything for refmac. For >> phenix.refine you will need to add a bond description to the .edit file for >> each linkage the IAS makes to the neighboring aas. >> >> You may take a look at the structure 1AT6 and its PDB file. The residue >> IAS 101 is an example of isoASP. Note that the IAS atoms are HETATM in the >> chain and there are two LINK records in the header to indicate its linkage >> to neighbouring aas (LINK records are normally not generated or needed >> during refinement using refmac or phenix.refine). >> >> >> Zhijie >> >> >> >> *From:* Xiao Lei <xiaoleiusc(a)gmail.com> >> *Sent:* Monday, August 17, 2015 6:50 PM >> *To:* PHENIX user mailing list <phenixbb(a)phenix-online.org> >> *Subject:* [phenixbb] Coot mutation of Asp residue to isoAsp residue >> >> Dear Phenixbb members, >> >> I suspect one Asp residue in my model may be an isoAsp (isomerization of >> Asp). I am asking if there is way to mutate Asp residue to >> isoAsp(isoaspartic acid) residue in coot GUI (I'm using coot 0.8.1 EL in >> Mac OS X10.10.5)? >> >> I know there is a mutation button on coot, but the mutated aa lists are >> all natural amino acids. If I have to delete the Asp residue first and then >> build isoAsp into the density map, is there a way in coot to build an >> isoAsp residue in map? >> >> Thanks ahead. >> >> Xiao >> >> ------------------------------ >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> >> >

9 years, 10 months

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